eGenomics: Cataloguing our complete genome collection

Abstract

The sessions of this workshop moved participant discussions from a broad view of the value and diversity of our current genome collection, to projects that are working to collect, present and analyse information from these genomes, to examples of how other communities have successfully driven standards development, to the specific consideration of the salient features of particular genomes. Speakers stimulated lively discussions throughout the workshop and most talks ran longer than expected because of probing questions from the audience. The proje cts described highlighted the diversity of taxa for which we have complete genomes and the growing importance of environmental and metagenomic data. They also highlighted that a number of initiatives are improving the quality of genomic descriptions available, but there is still a demand for curated information, which is best provided by those responsible for generating a given genome. The talks in the 'allied projects' session showed the group the benefits of learning from the experiences of other communities. The successful launch of a new genomic standard will take not only patience and enthusiasm from an international group of participants, but repeated meetings and funding. There was a strong sense of a shared mission among participants and an eagerness to offer solutions to ongoing issues in the area of metadata capture and presentation. For example, Matt Kane stressed in his talk that there is a considerable amount of environmental genetic data already in GenBank from targeted gene surveys, but the corresponding physicochemical and biogeochemical data can only be found by looking in the primary literature. Data from environmental genetic surveys requires the same metadata needed to maximize the usefulness of metagenomic information. Tatiana Tatusova of the NCBI volunteered to look into whether, as a first step towards this goal, sequences in GenBank that have been recovered directly from the environment could be logically grouped together by publication and in the future be tagged with additional metadata. The group expressed a shared vision of a future wh ere it would be routine to explore relationships between genomes, not only by taxonomy or traditional features such as shared proteins, but also by a wide variety of phenotypic, physiological, ecological or environmental attributes. Further, the group was extremely interested in the ability to harvest such data for the sake of populating their own databases and for large-scale comparative genomic analyses. Bergey's Manual was repeatedly mentioned as the preferred, definitive source of information about prokaryotic biology and taxonomy. There was much discussion and sharing of frustrations at the time and effort it took to curate even small amounts of information out of Bergey's Manual or the primary literature, despite the obvious value of having such organismal information tagged to genomic information. There was interest in the possibility of seeing the information in Bergey's Manual publicly available in electronic format. It was repeatedly mentioned that there is a need to harmonize across efforts, for example to work together to better distribute datasets and metadata, and there was special interest in the ability to share genomic annotations. It was hoped from the star t of this workshop that this group could come together to form a formal international consortium. This happened during the discussion sessions of Day Three, when participants of the workshop agreed to work together through virtual communication and future meetings towards recommendations on the type of information to capture, ways in which data can be more easily exchanged, and an implementation. Funding for future workshops has been secured in part in the form of a NERC International Opportunities Fund Award to DF (NE/3 521 773/1). The group is making an open call for new members to join the identified working groups dedicated to descriptions of different taxa (metagenomes, eukaryotes, prokaryotes, viruses, plasmids, and organelles) and concepts. Plans for future meetings and activities will be posted on the 'Cataloging our Current Genome Collection' website (http://www.genomics.ceh.ac.uk/genomecatalogue/). The draft checklist will also be available for community feedback. Anyone interested in knowing more about, or joining, this effort is encouraged to contact us. Copyright © 2006 John Wiley & Sons, Ltd.